First, Tuscans appear to have more shared derived variants with Vindija than Brits do. I can think of two explanations for this finding:

Higher genetic diversity in southern Europe compared to northern Europe; if these shared variants occurred at a low frequency in southern Europe vs. northern Europe to begin with, then genetic drift would have driven more of them to extinction in the north than in the south.

Possibility that the Vindija sequence has modern human admixture from a population of early Southern Europeans that would have contributed more to the gene pool of Tuscans (who are geographically quite close to Croatia) than to Brits

Second, North Chinese appear to be more similar to Neandertals than South Chinese are.

I am not entirely sure whether genetic drift would work in this case, since presumably CHB is representative of a larger Chinese population than Chinese settlers in Singapore.

A different explanation is that south Chinese may possess more admixture from an Asian type of erectus-like population that predates the common ancestor of modern humans and Neandertals, who almost certainly lived in the western end of Eurafrasian region.

Third, the Luhya from Kenya appear to have less Neandertal similarity than the Yoruba from Nigeria. This, of course, makes very little sense if Neandertal similarity can only be attributed to Neandertal admixture, since there were no Neandertals in Africa at all. Moreover, while the Luhya live in Kenya, their ultimate origins are further west, since they are a Bantu group, although they show mixed West/East African affiliations.

There are two alternatives:

Modern humans did originate in North-West Africa as the Y-chromosome phylogeny suggests, and East Africans possess some distinctive Palaeo-African ancestry from before the sapiens-Neandertal common ancestor.

Back-migration from Eurasia that affected different populations to different degrees; it is my impression, for example, that the Yoruba are almost completely a Y-haplogroup E population, but if anyone has any comparative results at hand, feel free to comment.

All in all, it will be interesting to see how the Vindija (and now Denisova) sequence compares to modern humans. The original papers could only compare against a handful of modern humans, but the availability of many full genomes from around the world will add statistical power to the comparisons.

Regarding the list posted by Crimson Guard, a large portion of 'Southern African' customers on 23andMe are Whites (Afrikaners etc) & Cape Coloureds, so the Neanderthal figure for that region is probably severely inflated.

^It is not impossible and in fact it seems Tuscans have more than Brits, but probably you'll find people discrediting this study because being the oldest in Europe it seems something that only Basque and North Europeans can claim.

"Third, the Luhya from Kenya appear to have less Neandertal similarity than the Yoruba from Nigeria. This, of course, makes very little sense if Neandertal similarity can only be attributed to Neandertal admixture, since there were no Neandertals in Africa at all."

There were Ibero-maurusians, who had more neanderthal blood than probably any other Hss when the sailed across to Morocco from Gibraltar during the LGM, according to their skeletal remains. Moroccans and Canary Islanders have genes they share only with the Basques and some Iberians, together with Afro-Asiatic mtdna haplogroup M1 (Afro-asiatic), J (Afro-asiatic and Basques), and y-dna haplogroup E (also Afro-asiatic). It would be interesting to see if these Algrians have these haplogroups too. The last neanderthal died on Gibraltar 21 ybp, the first Ibero-Maurusian shows up in Morocco soon after...

I'm 3/4 northern Italian and Tuscan. I'm 1/4 Central Italian. I am 3% Neanderthal on Geno 2.0 and 23andMe. My German/English husband is 2.6% Neanderthal. Thought I'd throw in real examples. I have talked to a few northern Italians on 23andMe and they are 3.4% or more Neanderthal. Recently, they think more mixing might have happened in Europe. Hawks has been tweeting about it as of May 2015.

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